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B-Cubed: Leveraging analysis-ready biodiversity datasets and cloud computing for timely and actionable biodiversity monitoring

Peter Desmet
October 10, 2023

B-Cubed: Leveraging analysis-ready biodiversity datasets and cloud computing for timely and actionable biodiversity monitoring

Talk at the TDWG 2023 annual conference - October 10, 2023.

Abstract: https://doi.org/10.3897/biss.7.110734

Recording: https://drive.google.com/file/d/1uDHhmp5zODZP5-Q78dENifWUAVr3D8Wu/view

Peter Desmet

October 10, 2023
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  1. Biodiversity Building Blocks for Policy
    B-Cubed
    Leveraging analysis-ready biodiversity
    datasets and cloud computing for timely
    and actionable biodiversity monitoring
    TDWG 2023, Hobart, Australia
    Peter Desmet

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  2. Biodiversity Building Blocks for Policy
    New Horizon Europe project

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  3. Biodiversity Building Blocks for Policy
    Opportunity
    Global biodiversity crisis
    requires rapid, reliable
    and repeatable
    biodiversity monitoring
    data which decision
    makers can use to
    evaluate policy.
    Challenge
    B-Cubed is
    standardizing access to
    biodiversity data,
    empowering
    policymakers to address
    the impacts of biodiversity
    change.
    Aim
    Such information – from
    local to global level and
    within relevant timescales
    – calls for an improved
    integration of data on
    biodiversity from
    different sources.

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  4. Biodiversity Building Blocks for Policy
    Essential Biodiversity
    Variables (EBV)
    ● Data cube with 3 dimensions
    ○ Taxonomic
    ○ Temporal
    ○ Spatial
    ● Each with extent, resolution
    and uncertainty
    ● Measurements (count)
    Kissling et al. (2018) doi.org/10.1111/brv.12359

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  5. Biodiversity Building Blocks for Policy
    Species occurrence cube
    SELECT
    taxon,
    year,
    round(lat) || '_' || round(lon)
    AS grid_cell,
    count(*)
    FROM
    occurrences
    GROUP BY
    taxon, year, grid_cell
    taxon year grid_cell count
    Vespa
    crabro
    2020 50_3 15
    Vespa
    crabro
    2020 50_4 14
    Vespa
    crabro
    2020 50_5 4
    Vespa
    crabro
    2020 51_3 20
    Vespa
    crabro
    2021 50_3 11
    Vespa
    crabro
    2021 50_4 9
    Vespa
    velutina
    2020 50_3 4
    Vespa
    velutina
    2020 50_4 2
    Vespa
    velutina
    2021 50_3 16
    Vespa
    velutina
    2021 50_4 5
    Desmet et al. (2023) bit.ly/D2_1_v1

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  6. Biodiversity Building Blocks for Policy
    Spatial grid assignment
    ● Spatial reference grid
    ○ EEA (1x1 km, 10x10 km)
    ○ QDGC (15x15 min, 30x30 min)
    ○ MGRS (1x1 m, 10x10 m)
    ● Assign occurrence to grid
    ○ Take into account uncertainty
    ○ Random assignment within
    uncertainty
    Oldoni et al. (2020)
    doi.org/10.1101/2020.03.23.983601

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  7. Biodiversity Building Blocks for Policy
    Spatial grid assignment
    SELECT
    taxon,
    year,
    eea_grid_code(
    lat, lon, coord_uncertainty,
    size = "10km",
    assignment = "random"
    ) AS grid_cell,
    count(*)
    FROM
    occurrences
    GROUP BY
    taxon, year, grid_cell
    taxon year grid_cell count
    Vespa
    crabro
    2020 10kmE380N3
    11
    2
    Vespa
    crabro
    2020 10kmE380N3
    12
    2
    Vespa
    crabro
    2020 10kmE380N3
    12
    0 (no row)
    Vespa
    crabro
    2020 10kmE381N3
    11
    5
    Vespa
    crabro
    2021 10kmE380N3
    11
    3
    Vespa
    crabro
    2021 10kmE380N3
    12
    2
    Vespa
    velutina
    2020 10kmE380N3
    11
    1
    Vespa
    velutina
    2020 10kmE380N3
    12
    1
    Vespa
    velutina
    2021 10kmE380N3
    11
    7
    Vespa
    velutina
    2021 10kmE380N3
    12
    2

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  8. Biodiversity Building Blocks for Policy
    SELECT
    taxon,
    year,
    count(*),
    count_higher(*, "genus")
    AS count_genus,
    FROM
    occurrences
    GROUP BY
    taxon, year
    Sampling bias taxon year count count_genu
    s
    Vespa
    crabro
    2020 15152 20361
    Vespa
    crabro
    2021 15055 20533
    Vespa
    crabro
    2022 20655 38641
    Vespa
    crabro
    2023 1805 7192
    Vespa
    velutina
    2020 3683 20361
    Vespa
    velutina
    2021 3825 20533
    Vespa
    velutina
    2022 16259 38641
    Vespa
    velutina
    2023 5108 7192

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  9. Biodiversity Building Blocks for Policy
    Using cubes in B-Cubed
    ● Modeled cubes
    ○ Suitability cube
    ○ Dissimilarity cube
    ○ Network invasibility cube
    ● Indicators
    ○ Phylogenetic indicators
    ○ Impact of alien taxa indicators
    ○ Robustness indicators

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  10. Biodiversity Building Blocks for Policy
    Automated
    workflows
    Cloud
    computing
    Policy aligned
    Tutorials Case studies FAIR and open

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  11. Biodiversity Building Blocks for Policy
    New GBIF download
    service
    ● Search & filter occurrences
    ○ Improved temporal processing
    ○ Filters to exclude occurrences
    ● Define cube
    ○ Dimensions
    ○ Output format (CSV, Parquet,
    NetCDF)
    ○ Destination (GBIF, cloud
    provider)
    ● DOI + Metadata

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  12. Biodiversity Building Blocks for Policy
    Hackathon
    ● Innovate with data cubes!
    ○ Interoperability with other data
    ○ Visualizations, integrations
    ○ Engage with the community
    ● Location: Brussels, Belgium
    ● Save the date: 2-5 April 2024

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  13. Biodiversity Building Blocks for Policy
    Thank you
    ● Presentation:
    bit.ly/tdwg-2023-b-cubed
    ● DOI: 10.3897/biss.7.110734
    ● Website: b-cubed.eu
    ● Twitter/X: @BCubedProject
    ● LinkedIn: B-Cubed Project
    Quentin Groom
    Laura Abraham
    Tim Adriaens
    Lissa Breugelmans
    David A. Clarke
    Miguel A. Fernández
    Louise Hendrickx
    Cang Hui
    Sabrina Kumschick
    Matilde Martini
    Melodie McGeoch
    Teodor Metodiev
    Joe Miller
    Co-authors
    Damiano Oldoni
    Henrique M. Pereira
    Cristina Preda
    Tim Robertson
    Duccio Rocchini
    Hanno Seebens
    Heliana Teixeira
    Maarten Trekels
    John R.Wilson
    Nikol Yovcheva
    Tsungai Zengeya
    Peter Desmet

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